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Sample GSM3840006 Query DataSets for GSM3840006
Status Public on Aug 09, 2019
Title CTCL1200.UNSORTED.OW.RNA
Sample type SRA
 
Source name Peripheral blood
Organism Homo sapiens
Characteristics cell markers: N/A
disease: PLL
hdaci group: Resistant
treatment: N/A
chip antibody: N/A
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol RNA was isolated from 0.5-2x106 cells stored in TRIzol reagent following manufacturer's instruction.
cDNA from total RNA was synthesized with a Clontech SMARTer low input RNA kit. An Illumina TruSeq preparation kit was used for library constructon per manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Base-calling was performed with bcl2fastq (v2.2.0). Adaptors were trimmed and RNA-seq reads were aligned to hg19 using UCSC knownGene annotations with STAR using default settings (v2.5.3a).
Read quantification was performed with Salmon (v0.11.0) with the parameters –fldMean 50 –fldSD 1 –seqBias and UCSC knownGene annotations.
Genes with fewer than 100 total counts were removed, and normalized abundance measurements were determined with DESeq2 (v1.20.0).
ChIP-seq reads were aligned to hg19 with bowtie2 (v2.2.5). Reads in ENCODE blacklist regions were removed with samtools (v1.3).
Peaks were called with MACS2 (v2.1.0.20150420) using parameters –q 0.01 –m 10 50 --nomodel --shiftsize=150 and input controls.
The consensus peak set, normalized peak signal, and differential peak binding were determined with diffBind (v2.8.0). chipSeeker (v1.16.1) was used to annotate peaks.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized gene-level abundance counts derived from DESeq2 are provided for each in RNAseq.NormalizedAbundance.txt. Normalized signal across consensus peak sets derived from DiffBind for both H3K9/14ac and H3K27ac are available in Resistant-v-Sensitive.H3AC.ConsensusPeaks.txt, Resistant-v-Sensitive.H3K27AC.ConsensusPeaks.txt, Romidepsin-v-Untreated.H3AC.ConsensusPeaks.txt, and Romidepsin-v-Untreated.H3K27AC.ConsensusPeaks.txt. Each row is a feature (gene or peak) and each column contains the normalized values for a given sample.
 
Submission date May 31, 2019
Last update date Aug 09, 2019
Contact name Jared Andrews
E-mail(s) jared.andrews@stjude.org
Organization name St. Jude Children's Research Hospital
Department Developmental Neurobiology
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platform ID GPL21290
Series (1)
GSE132053 Epigenetic Pathways of HDAC Inhibitor Resistance in Cutaneous T Cell Lymphoma
Relations
BioSample SAMN11917851
SRA SRX5944522

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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